Title: RNA folding kinetics and structure
Abstract: Specific physical forces define the folding landscape of large functional biopolymers like RNA and proteins. While it is generally agreed that the RNA folding landscape is comprised of multiple parallel pathways, how the reaction flux is partitioned among these pathways is still poorly understood. One approach to revealing the relationships between the physical forces that govern the folding reaction and the folding landscape is to quantitatively study the effect of solution condition and mutation on the partitioning of the flux through the different pathways. By adjusting the concentration of monovalent cations prior to addition of Mg2+, the initial (or unfolded) state of the molecule is changed. To assess the differences in the partitioning of flux through the folding pathways of the Tetrahymena thermophila group I intron, the Mg2+-induced folding reaction was perturbed by varying the initial concentration and type of monovalent cations. Clustering of hydroxyl radical time-progress curves followed by kinetic modeling using an exhaustive optimization procedure reveals a common kinetic model topology when Mg2+-mediated folding is conducted in the presence of either potassium or sodium containing solutions over a significant concentration range. Mutation of the L5b tertiary contact eliminates a kinetic intermediate, but the partitioning of the flux through the different pathways shows a similar dependence on monovalent cation concentration and type. The monovalent cation dependent differences are manifest by shifts in the flux of molecules through different folding pathways that are the result of changes in the relative stability of the folding intermediates. The fact that a common kinetic model underlies the folding reaction of the intron over a wide range of solution conditions suggests that the native state topology of the molecule defines the structure of the intermediates, while the electrostatic environment determines the relative stability of the different species in solution and thus the par-titioning of the folding flux.
